The intro to the track "WELCOME TO THE CITY" interpolates the chorus melody to "74", a 2018 song performed by J-pop singer Itoki Hana that Toby Fox had previously composed and provided guest vocals for.

After reaching the lobby of Queen's mansion in Chapter 2, if the player backtracks all the way back to and interacts with the very first save point in Cyber Field, the accompanying flavor text will change, noting how the player has already seen this area before riffing on how their backtracking served no real purpose whatsoever.

The track "Honksong.ogg", which plays during the traffic jam that prevents Kris from going past the Librarby in Chapter 2's prologue, interpolates excerpts from the Undertale tracks "Your Best Friend", "Spear of Justice", "Dogsong", and "Metal Crusher".

The dance that the miniature Sweet Cap'n Cakes doodles perform both when attacking and during their post-battle cutscene references "Danjo", a popular 2008 Vocaloid fan animation set to the 2006 song of the same name by Japanese artist Tarou.

When solving Cyber Field's typing puzzles in Chapter 2, stepping on an A key will, on rare occasions, play Sans' voice grunt instead of the usual text-to-speech clip.

If the player has a full equipment inventory when Spoiler:defeating Spamton NEO, he will give special dialogue lambasting Kris for this, noting how they most likely clogged their inventory on purpose before angrily running off. Spoiler:The Dealmaker/PuppetScarf can then be found in a chest en route to the basement's exit.

Within the data for the itch.io Mac 1.00 version of Chapter 2 is an early version of "Faint Courage", written in a lower key and lacking certain instrumental tracks compared to the final arrangement. The filename for this rendition is "audio_menu.ogg", implying that it was originally written for the Chapter 2 main menu before being refitted for the game over screen. The released game instead uses "Faint Glow" (which is replaced with "Before the Story" after completing the chapter), titled "menu.ogg" in the game's files, for the main menu. All other releases and revisions of Chapter 2 remove this unused song from the game's data.

Kris and Noelle are normally the only characters who can traverse the "DECEMBER" hallway in Cyber City, where their outlines appear while walking behind buildings in the foreground. Despite this, all other possible party members are programmed to display outlines if hacked into this area, including Berdly and the Original Starwalker, who can only normally appear as party members at the carnival (though they both use blue outlines like Kris instead of having color-coded ones like Noelle, Susie, and Ralsei).

In battle, Susie's UltimatHeal move is tied to her magic stat like most other spells, and consequently recovers more HP should the player boost her stats through hacking. However, in the cutscene where she first demonstrates it to Kris, it is hard-coded to only heal 2 HP regardless of circumstance.

On Twitter, Toby Fox revealed that he didn't know how people would receive the character of Spamton, and he even thought that he would be negatively received. His fears were exacerbated after the character got a disdainful and disgusted reaction from test players. However Spamton, nonetheless, turned out to be popular with fans and even garnered his own cult following with the massive sales and popularity of his merchandise not being able to meet demand at times.

The phone in Spamton's shop is hard-coded to ring in time with the shop's background music, "Dialtone". Hacking the game to turn off the song results in the phone remaining motionless indefinitely.

In the livestreamed playthrough of Chapter 1 conducted for Undertale's sixth anniversary, Toby Fox stated that he originally envisioned the game having a greater visual contrast between the Light World and Dark World, with the former looking "drab" and simplistic and the latter having more vibrant, detailed graphics in the vein of Chrono Trigger or Super Mario RPG: Legend of the Seven Stars.

Similarly, the Light World was at one point planned to be populated entirely by humans, and the Dark World entirely by monsters, with humans turning into monsters when they enter the latter. According to Fox, the idea was removed for "a lot of reasons," most prominently a desire to better distinguish the project from Undertale.

Within the data for Chapter 2 are unused graphics for an alternate, more detailed version of the scene where Ralsei heals Susie after the first Berdly fight. Among other things, these graphics depict Susie's hand bleeding, deviating from the established portrayal of monsters being made entirely from magic (and consequently lacking blood); it's likely that this contradiction is the reason why the graphics went unused.

It's possible to close the pop-up windows that appear during a Poppup's attacks using the mouse, functioning identically to closing an actual computer window.

In Chapter 2, Kris' eye can briefly be seen during the cutscene that plays whenever they and Susie enter a Dark World, appearing just before the pair plunge down at the end of the transition. This appears to nod to a graphical quirk present since Chapter 1, where the pixels in Kris' sprite will occasionally blend together while walking around, resulting in a red dot sometimes appearing in roughly the same area of their face by mistake.

Within the data for Chapter 2 is an unused alternate version of Spoiler:Spamton NEO's wasted turn, in which his phone fires a Pipis that explodes in his face and covers it in soot, rather than launching a volley of flying heads at him. Spamton NEO's head remains covered in soot until his next attack. It's likely that this event was changed due to Spoiler:its accidental resemblance to blackface, which historically was often paired with similar explosion gags in animation.

In the Japanese version of the game, the Spoiler:mock-VCR HUD icons that appear during Spamton NEO's ultimate attack in Chapter 2's Weird Route include two kanji-related puns: Spoiler:the "WRECK" icon and the "PAUSE" icon are respectively given the non-standard translations "殺エイ中" and "テイ死" instead of the typical "撮影中" and "ていし". The former includes an alternate reading of the kanji for "kill," while the latter uses the kanji for "death," tying in with Spoiler:Spamton's habit of replacing instances of "だい" and "です" with the phonetically-similar English words "die" and "death" throughout the Japanese script.

The Tasque enemies' quotes during battle are written in binary, with "me" representing a 1 and "ow" representing a 0. Translating most of these quotes gives each letter in the word "meow" (written in lowercase); meanwhile, the longer meow that Tasques utter after using the "Pet" ACT on them translates to a ♥ symbol.

The Version 1.07 patch adds in a new Easter egg surrounding Spoiler:the Pipis enemies that can be encountered on the Weird Route; entering a battle with one now has a 1% chance of spawning "Ms. Pipis", a Pipis with a pink bow on it. This difference is purely cosmetic, and the enemy functions identically to a standard Pipis. In the official notes for the patch, this Easter egg is alluded to by the text Spoiler:Pipis Fanservice, which is tucked in the bottom-right corner of the changelog.

Within the data for Chapter 2 is an unused attack for Spoiler:Spamton NEO in which the player is limited to shifting the SOUL between three horizontal planes while dodging oncoming oversized bullets. This attack functions identically to the Purple SOUL mechanic in Undertale, implying that at one point, Spoiler:the Spamton NEO fight was intended to be based around that rather than the Yellow SOUL mechanic.